Any decent Linux distribution comes with an installation option to automatically encrypt user's home directory. In case you do not wish to encrypt the entire home directory or perhaps you wish to encrypt some random directories on your Linux system you can use EncFS the FUSE-based cryptographic filesystem.
EncFS will allow you to encrypt and decrypt any directory in a matter of seconds. It will reside on top of your current filesytem and provide access to any EncFS encrypted directory only upon entering a correct predefined password. This short tutorial will show you how to encrypt and decrypt your directories with the EncFS cryptographic filesystem.